SMTL ID : 7aob.1

Crystal structure of Thermaerobacter marianensis malate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: A.158, R.159, N.162, V.163, F.165 Chain B: R.3, D.57 Chain D: D.244, R.245 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:R.159, B:R.3, B:R.3 Water bridges: D:D.244 GOL.5: 9 residues within 4Å: Chain A: N.13, A.16, A.17, F.227, F.228 Chain B: N.13, A.16, A.17, F.227 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.13, B:N.13 GOL.6: 7 residues within 4Å: Chain A: G.10, A.11, G.12, N.13, T.14, G.15, T.78 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.10, A:G.12, A:N.13, A:T.14, A:T.14, A:G.15, A:T.78 GOL.7: 4 residues within 4Å: Chain A: E.258, K.279, I.280, E.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.280, A:E.282 GOL.9: 8 residues within 4Å: Chain A: R.3, D.57 Chain B: A.158, N.162, V.163, F.165 Chain C: D.244, R.245 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Water bridges: C:D.244, B:N.162 Hydrogen bonds: B:A.158, A:R.3, A:R.3 GOL.10: 9 residues within 4Å: Chain B: D.244, R.245 Chain C: A.158, R.159, N.162, V.163, F.165 Chain D: R.3, D.57 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.3, D:R.3, C:R.159, C:N.162 Water bridges: C:N.162 GOL.12: 9 residues within 4Å: Chain A: D.244, R.245 Chain C: R.3, D.57 Chain D: A.158, R.159, N.162, V.163, F.165 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.3, C:R.3, D:A.158, D:R.159, D:N.162 GOL.13: 5 residues within 4Å: Chain D: T.78, G.80, A.81, T.120, N.121 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.121 Water bridges: D:T.14, D:S.225 GOL.14: 9 residues within 4Å: Chain C: N.13, A.16, A.17, F.227 Chain D: N.13, A.16, A.17, F.227, F.228 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.13, D:A.17, C:N.13

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: Q.41, T.61, G.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.41, A:G.62 PEG.4: 6 residues within 4Å: Chain A: D.34, V.35, Y.66, A.79, I.99, I.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.34, A:V.35

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 5 residues within 4Å: Chain A: R.159, E.160 Chain B: D.29, V.59, T.61 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.29, A:R.159, A:E.160

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: G.80, A.81, L.119, T.120, N.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.80, A:L.119, A:N.121

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 5 residues within 4Å: Chain C: R.159, R.209 Chain D: M.48, V.59, T.61 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.159, C:R.209 Water bridges: C:R.209, C:R.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertrand, Q. et al., Crystal structure of Thermaerobacter marianensis malate dehydrogenase. To Be Published

Release Date

2020-10-28

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Malate dehydrogenase